[BioC] loading processed data into eset class
zhliu.tju at gmail.com
Thu Aug 5 17:19:02 CEST 2010
Thanks a lot for your soon reply.
I think this processed data in arrayexpress is not background corrected and
normalized, though it should be as normalized in MIAME data format. Because
the CHP:singal amount vary greatly. For example as below, some of them are
less than 100 but some of them are over thousands.
I think they should be normalized. Also I checked the idf file and there is
not indication about the method about normalization. So is there any method
applicable to eset?
From: Alex Gutteridge [mailto:alexg at ruggedtextile.com]
Sent: 05 August 2010 15:59
To: Zhe Liu
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] loading processed data into eset class
On Thu, 5 Aug 2010 15:11:34 +0100, "Zhe Liu" <zhliu.tju at gmail.com> wrote:
> I have a problem with loading matrix data into eset class object. The
> data.frame is used to load tab-delimited processed data. But when I want
> run rma() method, there is always a error.
> Eset=new("ExpressionSet", phenoData=phenoData, featureData=featureData,
> experimentData=experimentData, exprs=as.matrix(arraydata_pro))
> when I run the final line, it reported:
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "probeNames", for
rma() works on AffyBatch objects and creates ExpressionSet objects - hence
If the data is already processed why do you want to run rma?
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